Purpose

The purpose of this document is to track and provide instructions for reproducing the analyses of the Wester Redcedar Dieback Map project data.

Approach

The overall approach is to model empirical data collected by community scientists with ancillary environmental data (climate, topographic, and soils) to identify important predictors of western redcedar dieback.

Open questions

The below bullets are questions or comments that should be resolved before final analyses

  • Considerations
    • Should we filter data to remove GPS points with poor accuracy?
    • Data averaged over last decade or last 30 years?
    • Better approach to calculate topographic data?
    • Should we restrict data to Washington and Oregon because that is where soils data is available.
    • Should we look at data from last decade only or also from last 30 years?

Notes

  • Important notes to consider when visualizing these data.
    • Observations are filtered to only include those with Soils Data
    • Data is filtered to show most common symptoms only.

Data

The data used in the below visualizations are described in the Data Wrangle folder.

## # A tibble: 11 × 2
## # Groups:   field.tree.canopy.symptoms [11]
##    field.tree.canopy.symptoms                             n
##    <fct>                                              <int>
##  1 Branch Dieback or 'Flagging'                          19
##  2 Browning Canopy                                       19
##  3 Extra Cone Crop                                        2
##  4 Healthy                                              403
##  5 Multiple Symptoms (please list in Notes)              17
##  6 New Dead Top (red or brown needles still attached)    33
##  7 Old Dead Top (needles already gone)                   83
##  8 Other (please describe in Notes)                       8
##  9 Thinning Canopy                                      118
## 10 Tree is dead                                          37
## 11 Yellowing Canopy                                      10
## # A tibble: 5 × 2
## # Groups:   field.tree.canopy.symptoms [5]
##   field.tree.canopy.symptoms                             n
##   <fct>                                              <int>
## 1 Healthy                                              403
## 2 New Dead Top (red or brown needles still attached)    33
## 3 Old Dead Top (needles already gone)                   83
## 4 Thinning Canopy                                      118
## 5 Tree is dead                                          37
## # A tibble: 2 × 2
## # Groups:   field.tree.canopy.symptoms [2]
##   field.tree.canopy.symptoms     n
##   <fct>                      <int>
## 1 Healthy                      403
## 2 Unhealthy                    346

Data Visualization

Climate

Decade 2011-2020

MAT
Symptoms

Site Severity
Size Class
MAP

AHM

SHM

Filtered SHM <200

MSP

CMD

Eref

CMI_sp
Symptoms

Site Severity
Size Class

TOPO Data

Aspect

## Warning: Removed 4 rows containing non-finite values (stat_boxplot).

Slope

## Warning: Removed 4 rows containing non-finite values (stat_boxplot).

Elevation

## Warning: Removed 4 rows containing non-finite values (stat_boxplot).

Topo & Climate

Slope
CMD
## Warning: Removed 4 rows containing missing values (geom_point).

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 4 rows containing non-finite values (stat_smooth).

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 4 rows containing non-finite values (stat_smooth).

Elevation
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 4 rows containing non-finite values (stat_smooth).

Soils Data

Bedrock Depth

## Warning: Removed 621 rows containing non-finite values (stat_boxplot).

drclasscd

drclasswettest

hydgrpdcd

slopegradwta

## Warning: Removed 33 rows containing non-finite values (stat_boxplot).

niccdcdpct

## Warning: Removed 3 rows containing non-finite values (stat_boxplot).

Binary Data

Climate

MAT

Site Severity
Size Class

MAP

AHM

SHM

Filtered SHM <200

MSP

CMD

Eref

CMI_sp

Topo

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 6 rows containing non-finite values (stat_smooth).

## Warning: Removed 6 rows containing non-finite values (stat_boxplot).

Soils

Bedrock Depth

## Warning: Removed 688 rows containing non-finite values (stat_boxplot).

drclasscd

drclasswettest

hydgrpdcd

slopegradwta

## Warning: Removed 38 rows containing non-finite values (stat_boxplot).

niccdcdpct

## Warning: Removed 4 rows containing non-finite values (stat_boxplot).

component_taxgrtgroup

#### component_taxpartsize

## NULL

muaggatt_wtdepaprjunmin

Water Table Depth - April - June - Minimum

##  int [1:749] 45 23 NA NA NA NA 0 NA NA NA ...
## Warning: Removed 441 rows containing non-finite values (stat_boxplot).